Package: bamsignals 1.45.1

Johannes Helmuth

bamsignals: Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Authors:Alessandro Mammana [aut, cre], Johannes Helmuth [aut]

bamsignals_1.45.1.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
bamsignals/json (API)
NEWS

# Install 'bamsignals' in R:
install.packages('bamsignals', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lamortenera/bamsignals/issues

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:bamsignals-1.45.1(bioc 3.24)bamsignals-1.44.1(bioc 3.23)

dataimportsequencingcoveragealignmentcurlbzip2xz-utilszlibcpp

8.63 score 15 stars 9 packages 2.1k downloads 5 mentions 6 exports 8 dependencies

Last updated from:80ce5c52a4. Checks:1 NOTE, 12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE172
linux-devel-arm64OK238
linux-devel-x86_64OK271
source / vignettesOK223
linux-release-arm64OK277
linux-release-x86_64OK230
macos-release-arm64OK145
macos-release-x86_64OK287
macos-oldrel-arm64OK152
macos-oldrel-x86_64OK261
windows-develOK222
windows-releaseOK217
windows-oldrelOK226
wasm-releaseFAIL150

Exports:alignSignalsas.listbamCountbamCoveragebamProfilewidth

Dependencies:BiocGenericsgenericsGenomicRangesIRangesRcppRhtslibS4VectorsSeqinfo

Introduction to the bamsignals package

Alessandro Mammana and Johannes Helmuth

Rendered frombamsignals.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2016-04-11
Started: 2015-02-13

Readme and manuals

Help Manual

Help pageTopics
Converts the container to a list 'l' such that 'l[[i]]' is the i-th signal.as.list.CountSignals
Efficient counting of reads in a bam filebamsignals-package bamsignals
Functions for extracting count signals from a bam file.bamCount bamCount,character,GenomicRanges-method bamCoverage bamCoverage,character,GenomicRanges-method bamProfile bamProfile,character,GenomicRanges-method bamsignals-methods
Container for count signalsalignSignals alignSignals,CountSignals-method as.list as.list,CountSignals-method CountSignals CountSignals-class length length,CountSignals-method width width,CountSignals-method [,CountSignals,ANY-method